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miRTex

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) regulate a wide range of cellular and developmental processes through gene expression suppression or mRNA degradation. Experimentally validated miRNA gene targets are often reported in the literature. In this paper, we describe miRTex, a text mining system that extracts miRNA-target relations, as well as miRNA-gene and gene-miRNA regulation relations. The system achieves good precision and recall when evaluated on a literature corpus of 150 abstracts with F-scores close to 0.90 on the three different types of relations.

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miRegulome

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

miRNAs regulate post transcriptional gene expression by targeting multiple mRNAs and hence can modulate multiple signalling pathways, biological processes, and patho-physiologies. Therefore, understanding of miRNA regulatory networks is essential in order to modulate the functions of a miRNA. The focus of several existing databases is to provide information on specific aspects of miRNA regulation. However, an integrated resource on the miRNA regulome is currently not available to facilitate the exploration and understanding of miRNA regulomics.

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mRTP

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs are a class of small endogenous noncoding RNAs which play important regulatory roles mainly by post-transcriptional depression. Finding miRNA target genes will help a lot to understand their biological functions. We developed an ensemble machine learning algorithm which helps to improve the prediction of miRNA targets. The performance was evaluated in the training set and in FMRP associated mRNAs. Moreover, using human mir-9 as a test case, our classification was validated in 9 of 15 transcripts tested.

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miRiam

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are small RNA molecules that modulate gene expression through degradation of specific mRNAs and/or repression of their translation. miRNAs are involved in both physiological and pathological processes, such as apoptosis and cancer. Their presence has been demonstrated in several organisms as well as in viruses. Virus encoded miRNAs can act as viral gene expression regulators, but they may also interfere with the expression of host genes. Viral miRNAs may control host cell proliferation by targeting cell-cycle and apoptosis regulators.

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SoMART

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Plant microRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) play important roles in a variety of biological processes. Bioinformatics prediction and small RNA (sRNA) cloning are the most important approaches for identification of miRNAs and tasiRNAs and their targets. However, these approaches are not readily accessible to every researcher. Here we present SoMART, a web server for miRNA/tasiRNA analysis resources and tools, which is designed for researchers who are interested in identifying miRNAs or tasiRNAs that potentially regulate genes of interest.

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AltAnalyze and DomainGraph

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Alternative splicing is an important mechanism for increasing protein diversity. However, its functional effects are largely unknown. Here, we present our new software workflow composed of the open-source application AltAnalyze and the Cytoscape plugin DomainGraph. Both programs provide an intuitive and comprehensive end-to-end solution for the analysis and visualization of alternative splicing data from Affymetrix Exon and Gene Arrays at the level of proteins, domains, microRNA binding sites, molecular interactions and pathways.

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targetHub

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

With the expansion of high-throughput technologies, understanding different kinds of genome-level data is a common task. MicroRNA (miRNA) is increasingly profiled using high-throughput technologies (microarrays or next-generation sequencing). The downstream analysis of miRNA targets can be difficult. Although there are many databases and algorithms to predict miRNA targets, there are few tools to integrate miRNA-gene interaction data into high-throughput genomic analyses.

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miR2GO

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

miR2GO is a web-based platform for comparative analyses of human miRNA functions. It includes two programs: miRmut2GO and miRpair2GO. miRmut2GO implements a knowledge-based method to assess the functional effects of genetic and somatic mutations in microRNA seed regions. The functional effects of a mutation are analysed by semantic comparison of enriched gene ontology (GO) annotations of the target gene sets for the wild-type and mutated alleles.

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DualTargeting

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

We have developed an algorithm for the prediction of dual-targeting short interfering RNAs (siRNAs) in which both strands are deliberately designed to separately target different mRNA transcripts with complete complementarity. An advantage of this approach versus the use of two separate duplexes is that only two strands, as opposed to four, are competing for entry into the RNA-induced silencing complex.

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vHoT

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Some viruses have been reported to transcribe microRNAs, implying complex relationships between the host and the pathogen at the post-transcriptional level through microRNAs in virus-infected cells. Although many computational algorithms have been developed for microRNA target prediction, few have been designed exclusively to find cellular or viral mRNA targets of viral microRNAs in a user-friendly manner. To address this, we introduce the viral microRNA host target (vHoT) database for predicting interspecies interactions between viral microRNA and host genomes.

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